Abstract
In this study, we wanted to inspect whether the evolutionary driven differences in primary sequences could correlate, and thus predict the genetic diversity of related marker loci, which is an important criterion to assess the quality of any DNA marker. We adopted new approach of quantitative symbolic DNA sequence analysis called DNA random walk representation to study multiallelic marker loci from Begonia × tuberhybrida Voss. We described significant correlation of random walk-derived digital invariants to genetic diversity of the marker loci. Specifically, on the 3D-contour plot of multivariate principal component analysis (PCA), we revealed statistical correlation between the first two PCA factors and the number of alleles per marker locus. Based on that correlation, we suggest that DNA walk representation may predict allele-rich loci solely from their primary sequences, which improves current design of new DNA germplasm identificators.
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Abbreviations
- PCA:
-
pricipal component analysis
References
Bai, F-L., Liu, Y-Z., Wang, T-M.: A representation of DNA primary sequences by random walk. — Math. Biosci. 209: 282–291, 2007.
Berger, J.A., Mitra, S.K., Carli, M., Neri, A.: Visualization and analysis of DNA sequences using DNA walks. — J. Franklin. Inst. Eng. Appl. Math. 341: 37–53, 2004.
Cordeiro, A.I., Sanchez-Sevilla, J.F., Alvarez-Tinaut, M.C., Gomez-Jimenez, M.C.: Genetic diversity assessment in Portugal accessions of Olea europaea by RAPD markers. — Biol. Plant 52: 642–647, 2008.
Dodin, G., Pierre, V., Levoiretal, P.: Fourier and wavelet transform analysis: a tool for visualizing regular patterns in DNA sequences. — J. theor. Biol. 206: 323–326, 2000.
Griga, M., Horáček, J., Klenotičová, H.: Protein patterns associated with Pisum sativum somatic embryogenesis. — Biol. Plant. 51: 201–211, 2007.
Li, H., Zhang, S.G., Gao, J.M., Wang, C.G., Zhang, Y., Qi, L.W., Chen, L., Song, W. Q.: Development of a sequence characterized amplified region (SCAR) marker associated with high rooting ability in Larix. — Biol. Plant. 52: 525–528, 2008.
Nandy, A., Harle, M., Basak, S.C.: Mathematical descriptors of DNA sequences: development and applications. — Arkivoc 9: 211–238, 2006.
Nandy, A., Basak, S.C., Gute, B.D.: Graphical representation and numerical characterization of H5N1 avian flu neuraminidase gene sequence. — J. Chem. Inform. Model. 47: 945–951, 2007.
Peng, C.-K., Buldyrev, S.V., Goldberger, A.L., Havlin, S., Sciortino, F., Simons, M., Stanley, H.E.: Long-range correlations in nucleotide sequences. — Nature 356: 168–170, 1992.
Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., Lehväslaiho, H., Matsalla, C., Mungall, C.J., Osborne. B.I., Pocock, M.R., Schattner, P., Senger, M., Stein, L.D., Stupka, E., Wilkinson, M.D., Birney, E.: The Bioperl toolkit: Perl modules for the life sciences. — Genome Res. 12: 1611–1618, 2002.
Tsonis, A.A., Kumar, P., Elsner, J.B., Tsonis, P.A.: Wavelet analysis of DNA sequences. — Phys. Rev. E 53: 1828–1834, 1996.
Wiesner, I., Wiesnerova, D.: Sequence characterized markers from Begonia × tuberhybrida Voss. — Eur. J. hort. Sci. 73: 244–247, 2008.
Acknowledgements
This study was supported by the program of Targeted Research DP3-PP2 of the National Research Program, project No. 1QS500510566 of the Academy of Sciences of the Czech Republic, and by the project AV CR No. VZ-AVOZ 50510513. We thank Jan Wiesner for technical assistance.
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Wiesner, I., Wiesnerová, D. 2D random walk representation of Begonia × tuberhybrida multiallelic loci used for germplasm identification. Biol Plant 54, 353–356 (2010). https://doi.org/10.1007/s10535-010-0062-7
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DOI: https://doi.org/10.1007/s10535-010-0062-7